Suite2p: beyond 10,000 neurons with standard two-photon microscopy

TLDR

Two‑photon calcium imaging now records vast neuronal populations, but existing computational pipelines are inefficient and produce hard‑to‑interpret results. The authors present Suite2p, a fast, accurate pipeline that registers movies, detects cells, extracts calcium traces, and infers spike times. Suite2p processes raw two‑photon movies by registering frames, detecting active cells, extracting calcium traces, and inferring spike times. Suite2p runs on standard workstations, operates faster than real time, recovers roughly twice as many cells as the previous state‑of‑the‑art method, and its low computational load enables routine detection of about 10,000 cells simultaneously with standard two‑photon resonant‑scanning microscopes, promising to reveal fine structure of activity in large neuronal populations or subcellular structures such as synaptic boutons.

Abstract

Abstract Two-photon microscopy of calcium-dependent sensors has enabled unprecedented recordings from vast populations of neurons. While the sensors and microscopes have matured over several generations of development, computational methods to process the resulting movies remain inefficient and can give results that are hard to interpret. Here we introduce Suite2p: a fast, accurate and complete pipeline that registers raw movies, detects active cells, extracts their calcium traces and infers their spike times. Suite2p runs on standard workstations, operates faster than real time, and recovers ~2 times more cells than the previous state-of-the-art method. Its low computational load allows routine detection of ~10,000 cells simultaneously with standard two-photon resonant-scanning microscopes. Recordings at this scale promise to reveal the fine structure of activity in large populations of neurons or large populations of subcellular structures such as synaptic boutons.